Mikaeel’s mother Rosdeep reported him missing on Thursday morning, claiming he’d vanished overnight and hadn’t been seen since she’d put him to bed.
The bungalow in Fife where he was found is said to belong to Mikaeel’s aunt, his mother’s sister.
Rosdeep has been detained in connection with Mikaeel’s disappearance.
Police have sectioned off the bungalow and an investigation will now take place.
During a 1am press briefing this morning, Assistant Chief Constable Malcolm Graham confirmed the finding of Mikaeel’s body.
He said: “The investigation into the disappearance of Mikaeel Kular has been wide-ranging and fast moving.
“As a result of the inquiries the body of a young child was recovered in Fife just before midnight. We strongly believe this is the body of Mikaeel.
“A person has been detained in connection with the recovery of the body and members of Mikaeel’s family have been informed.
“Our thoughts and sympathies are with them at this time.”
Hundreds of volunteers had joined the search for Mikaeel, some of them searching all night in freezing temperatures for the missing boy.
It has been reported that police have also cordoned off the woodland around the Fife bungalow and the forensics team had been on the scene.
A memorial service for Mikaeel will be held tonight at 7pm.